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- PDB-7o7d: Crystal structure of rsEGFP2 mutant V151A in the fluorescent on-s... -

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Basic information

Entry
Database: PDB / ID: 7o7d
TitleCrystal structure of rsEGFP2 mutant V151A in the fluorescent on-state determined by synchrotron radiation at 100K
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Reversibly photoswitchable fluorescent protein
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsWoodhouse, J. / Adam, V. / Hadjidemetriou, K. / Colletier, J.-P. / Weik, M.
CitationJournal: Chemphyschem / Year: 2022
Title: Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement.
Authors: Adam, V. / Hadjidemetriou, K. / Jensen, N. / Shoeman, R.L. / Woodhouse, J. / Aquila, A. / Banneville, A.S. / Barends, T.R.M. / Bezchastnov, V. / Boutet, S. / Byrdin, M. / Cammarata, M. / ...Authors: Adam, V. / Hadjidemetriou, K. / Jensen, N. / Shoeman, R.L. / Woodhouse, J. / Aquila, A. / Banneville, A.S. / Barends, T.R.M. / Bezchastnov, V. / Boutet, S. / Byrdin, M. / Cammarata, M. / Carbajo, S. / Eleni Christou, N. / Coquelle, N. / De la Mora, E. / El Khatib, M. / Moreno Chicano, T. / Bruce Doak, R. / Fieschi, F. / Foucar, L. / Glushonkov, O. / Gorel, A. / Grunbein, M.L. / Hilpert, M. / Hunter, M. / Kloos, M. / Koglin, J.E. / Lane, T.J. / Liang, M. / Mantovanelli, A. / Nass, K. / Nass Kovacs, G. / Owada, S. / Roome, C.M. / Schiro, G. / Seaberg, M. / Stricker, M. / Thepaut, M. / Tono, K. / Ueda, K. / Uriarte, L.M. / You, D. / Zala, N. / Domratcheva, T. / Jakobs, S. / Sliwa, M. / Schlichting, I. / Colletier, J.P. / Bourgeois, D. / Weik, M.
History
DepositionApr 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 19, 2022Group: Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen / pdbx_struct_mod_residue
Item: _citation.journal_id_ISSN / _citation.journal_volume / _entity_src_gen.gene_src_common_name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,5041
Polymers28,5041
Non-polymers00
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-2 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.990, 62.090, 69.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein


Mass: 28504.148 Da / Num. of mol.: 1
Mutation: M1_S2insV, F64L, S65T, H231L, A206K, Q69L, V163S, T65A, V150A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES pH 7.8 - 8.4 and 1.7 - 2.4 M ammonium sulfate
PH range: 7.8 - 8.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.4→46.28 Å / Num. obs: 42980 / % possible obs: 97.4 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rrim(I) all: 0.048 / Net I/σ(I): 17.26
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 3.9 % / Num. unique obs: 2669 / CC1/2: 0.853 / Rrim(I) all: 0.425 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DTX

5dtx


Resolution: 1.4→46.28 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 2150 5 %
Rwork0.1521 40830 -
obs0.1535 42980 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.51 Å2 / Biso mean: 18.3382 Å2 / Biso min: 7.14 Å2
Refinement stepCycle: final / Resolution: 1.4→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 0 353 2204
Biso mean---32.34 -
Num. residues----232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.430.25391410.2182669281097
1.43-1.470.25091410.21042677281897
1.47-1.510.24051420.19272691283398
1.51-1.550.21011400.17892676281697
1.55-1.60.20041430.1682707285098
1.6-1.660.20871440.1642729287399
1.66-1.730.18471430.15682723286698
1.73-1.80.16981430.14932710285398
1.8-1.90.15061440.14722744288898
1.9-2.020.13851430.13622727287099
2.02-2.180.16251460.14042760290698
2.18-2.390.1951440.14882741288597
2.39-2.740.1891450.1552755290098
2.74-3.450.16961450.14682750289596
3.45-46.280.16831460.14052771291793

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